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Try this http://tools.cisco.com/search/results/display?url=http%3a%2f%2fwww.cisco.com%2fc%2fdam%2fen%2fus%2fproducts%2fcollateral%2fswitches%2fnexus-4000-series-switches%2f6701_catswitch_guide_v7_r5.pdf&pos=5&query=WS-C3524-XL-EN

Make sure that the frame encapsulation is set on the router to 802.1q on each of the sub-interfaces. You could also try fixing the speed and duplex on both the router and the switch in case there is a problem negotiating the speed and duplex.

%SYS-4-P2_WARN: 1/Tag 0
The switch generates %SYS-4-P2_WARN: 1/Tag
0… messages.
This example shows the syslog output that you see when this error
occurs:
%SYS-4-P2_WARN: 1/Tag [dec] on packet from [ether] port [chars], but port's native vlan is [dec]
This message indicates that an 802.1Q-tagged packet was received on a
nontrunk port. The VLAN that is derived from the packet tag is different from
the port native VLAN. In the error message:

The Tag [dec] is the VLAN identifier
from the packet.

The [ether] is the host MAC
address.

The port [chars] is the port
identifier.

The second [dec] is the native VLAN
number.

There is a possibility that the local port is incorrectly configured
as an access port instead of a trunk port. Alternately, the remote side can
have been configured as a trunk port instead of an access port.
Verify that the local port is not incorrectly configured as an access
port instead of a trunk port. Also, verify that the remote side is not
configured as a trunk port instead of an access port.

When you say you were able to connect to the switch through hyperterm, were you able to login with the enable password?
If not, you cannot reset the factory defaults without the enable password.
If you do not have this then search on Cisco's site for password recovery for your model switch.
If you did login with the enable password, the command to run for CATos is "clear config all".
For Cisco IOS, you have the right command with "write erase". When you issue that command, do you get a "Erase of nvram: complete
" or an error?
Are you issuing the "reload" command after a successful erase?
Be sure you answer No when it asks "System configuration has been modified. Save? [yes/no]:" as sometimes this seems misleading and some people think they mean to save the reloaded default.
They are really warning you that you are about to loose the old configuration and attempting to prevent you from accidently erasing it. So answer "no".
After a successful reload of the IOS you should also clear any VLAN information.
To do this, issue "delete flash:vlan.dat" and then do another "reload".